Properties
| Property | Description | Data Type |
|---|---|---|
|
protocol_identifier
required |
Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412. |
<
string
>
|
|
allowed_collection_event_names
required |
Allowed values for sample.json#properties/collection_event_name for this trial. |
<
array
>
|
|
allowed_cohort_names
required |
Allowed values for sample.json#properties/cohort_name for this trial. |
<
array
>
|
|
participants
required |
The collection of all data related to a specific participant in the context of a specific clinical trial. |
<
array
>
|
| nct_id | ClinicalTrials.gov identifier. Example: NCT03731260. |
<
string
>
|
| nci_id | NCI Trial Identifier. Example: NCI22345. |
<
string
>
|
| trial_name | Name of clinical trial. |
<
string
>
|
| trial_description | A brief description of the clinical trial. |
<
string
>
|
| trial_organization | Name of the primary organization that oversees the clinical trial. Example: ECOG-ACRIN, SWOG, etc. |
<
string
>
|
| grant_or_affiliated_network | The primary organization providing grant funding and supporting the trial. |
<
string
>
|
| trial_status | What stage the clinical trial is at in its process. |
<
string
>
|
| biobank | The primary organization responsible for storing biospecimens from this study. |
<
string
>
|
| lead_cimac_pis | The PI(s) from the CIMAC-CIDC network responsible for this study. |
<
array
>
|
| lead_cimac_contacts | A list of contacts for this trial. |
<
array
>
|
| lead_trial_staff | The names of lead trial staff members other than the PIs. |
<
array
>
|
| justification | A description of the reasons why this study could provide insight into molecular biomarkers of immunotherapy. |
<
string
>
|
| schema | Information about an image file. | artifacts.artifact_image |
| biomarker_plan | A description of the objectives and hypotheses for the proposed biomarkers. |
<
string
>
|
| data_sharing_plan | A description of the rules governing data sharing and publications. |
<
string
>
|
| collection_event_list | A list associating collection events with allowed sample types. |
<
array
>
|
| shipments |
<
array
>
|
|
| assays | Reference for every available assay in network. | assays.components.available_assays |
| analysis | Reference for every available assay in network. | assays.components.available_ngs_analyses |
| clinical_data | Clinical data recorded for a clinical trial | clinical_data |
clinical_trial.full.json
{
"$id": "clinical_trial",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Encapsulates information regarding a clinical trial.",
"properties": {
"allowed_cohort_names": {
"$comment": "This works together with sample.json#properties/cohort_name/in_doc_ref_pattern.",
"description": "Allowed values for sample.json#properties/cohort_name for this trial.",
"items": {
"type": "string"
},
"type": "array"
},
"allowed_collection_event_names": {
"$comment": "This works together with sample.json#properties/collection_event_name/in_doc_ref_pattern.",
"description": "Allowed values for sample.json#properties/collection_event_name for this trial.",
"items": {
"type": "string"
},
"type": "array"
},
"analysis": {
"$id": "available_ngs_analyses",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Reference for every available assay in network.",
"mergeStrategy": "objectMerge",
"properties": {
"rna_analysis": {
"$id": "rna_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Combined analysis files for the whole RNAseq assay.",
"properties": {
"level_1": {
"items": {
"$id": "rna_level1_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "RNAseq assay output files for a sample level 1 analysis.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"fusion": {
"$id": "fusion",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Fusion output sample files.",
"properties": {
"fusion_predictions": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
}
},
"required": [
"fusion_predictions"
],
"title": "RNAseq Fusion Output Files",
"type": "object"
},
"microbiome": {
"$id": "microbiome",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Microbiome output sample files.",
"properties": {
"sample_report": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"sample_report"
],
"title": "RNAseq Microbiome Output Files",
"type": "object"
},
"msisensor": {
"$id": "msisensor",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Msisensor output sample files.",
"properties": {
"msisensor_report": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"msisensor_report"
],
"title": "RNAseq msisensor Output Files",
"type": "object"
},
"neoantigen": {
"$id": "neoantigen",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Neoantigen output sample files.",
"properties": {
"genotype": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"genotype"
],
"title": "RNAseq Neoantigen Output Files",
"type": "object"
},
"rseqc": {
"$id": "star",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Star output sample files.",
"properties": {
"read_distrib": {
"$id": "binary_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a binary file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BINARY",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Binary Artifact",
"type": "object"
},
"tin_score": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tin_score_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"read_distrib",
"tin_score_summary",
"tin_score"
],
"title": "RNAseq Star Output Files",
"type": "object"
},
"salmon": {
"$id": "star",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Star output sample files.",
"properties": {
"aux_info_ambig_info_tsv": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"aux_info_expected_bias": {
"$id": "gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a GZ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "GZ Artifact",
"type": "object"
},
"aux_info_fld": {
"$id": "gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a GZ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "GZ Artifact",
"type": "object"
},
"aux_info_meta_info": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
},
"aux_info_observed_bias": {
"$id": "gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a GZ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "GZ Artifact",
"type": "object"
},
"aux_info_observed_bias_3p": {
"$id": "gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a GZ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "GZ Artifact",
"type": "object"
},
"cmd_info": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
},
"quant_sf": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"salmon_quant_log": {
"$id": "log_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a log file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "LOG",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "LOG Artifact",
"type": "object"
},
"transcriptome_bam_log": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"quant_sf",
"transcriptome_bam_log",
"aux_info_ambig_info_tsv",
"aux_info_expected_bias",
"aux_info_fld",
"aux_info_meta_info",
"aux_info_observed_bias",
"aux_info_observed_bias_3p",
"cmd_info",
"salmon_quant_log"
],
"title": "RNAseq Star Output Files",
"type": "object"
},
"star": {
"$id": "star",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Star output sample files.",
"properties": {
"chimeric_out_junction": {
"$id": "junction_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JUNCTION file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JUNCTION",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JUNCTION Artifact",
"type": "object"
},
"sorted_bam": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"sorted_bam_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"sorted_bam_stat_txt": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"transcriptome_bam": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
}
},
"required": [
"sorted_bam",
"sorted_bam_index",
"sorted_bam_stat_txt",
"transcriptome_bam",
"chimeric_out_junction"
],
"title": "RNAseq Star Output Files",
"type": "object"
},
"trust4": {
"$id": "trust4",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Trust4 output sample files.",
"properties": {
"trust4_report": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
}
},
"required": [
"trust4_report"
],
"title": "RNAseq Trust4 Output Files",
"type": "object"
}
},
"required": [
"cimac_id",
"star",
"rseqc",
"salmon",
"microbiome",
"trust4",
"neoantigen",
"msisensor",
"fusion"
],
"title": "RNAseq Level 1 Sample Analysis Output Files",
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"title": "RNAseq analysis combined files",
"type": "object"
},
"tcr_analysis": {
"$id": "tcr_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Output files generated from the TCRseq assay: TRA and TRB clones",
"properties": {
"batches": {
"items": {
"$id": "tcr_single_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Output files generated from the TCRseq assay: TRA and TRB clones",
"properties": {
"batch id": {
"description": "TCRseq batch identification number.",
"type": "string"
},
"records": {
"items": {
"$id": "tcr_pair_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Output files generated from the TCRseq assay: TRA and TRB clones",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"tra_clone": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"trb_clone": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"title": "TCRseq analysis TRA/TRB clone output files",
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"report_trial": {
"$id": "gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a GZ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "GZ Artifact",
"type": "object"
},
"summary_info": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"title": "TCR Output Files",
"type": "object"
},
"mergeOptions": {
"idRef": "/batch id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"title": "TCR Output Files",
"type": "object"
},
"wes_analysis": {
"$id": "wes_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Combined analysis files for the whole WES assay.",
"properties": {
"pair_runs": {
"items": {
"$id": "wes_pair_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Whole Exome Sequencing assay output files for a tumor normal pair of samples.",
"properties": {
"clonality": {
"$id": "WES Clonality Output Files",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Clonality output files.",
"properties": {
"clonality_pyclone": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"clonality_table": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
}
},
"required": [
"clonality_pyclone",
"clonality_table"
],
"title": "Clonality output files",
"type": "object"
},
"copynumber": {
"$id": "copynumber",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Copy number output files.",
"properties": {
"copynumber_cnv_calls": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"copynumber_cnv_calls_tsv": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
}
},
"required": [
"copynumber_cnv_calls",
"copynumber_cnv_calls_tsv"
],
"title": "WES Copynumber Output Files",
"type": "object"
},
"corealignments": {
"$id": "corealignments",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Core-alignments output files.",
"properties": {
"tn_corealigned": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"tn_corealigned_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [],
"title": "WES Corealignment Output Files",
"type": "object"
},
"msisensor": {
"$id": "msisensor",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "MSISensor2 output files.",
"properties": {
"msisensor": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"msisensor"
],
"title": "WES MSISensor2 Output Files",
"type": "object"
},
"neoantigen": {
"$id": "neoantigen",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Neoantigen output files.",
"properties": {
"HLA_results": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"combined_filtered": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"mhc_class_II_epitopes": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"mhc_class_II_filtered_condensed_ranked": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"mhc_class_I_epitopes": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"mhc_class_I_filtered_condensed_ranked": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
}
},
"required": [
"HLA_results",
"combined_filtered"
],
"title": "WES Neoantigen Output Files",
"type": "object"
},
"normal": {
"$id": "wes_sample_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Sample wise analysis files for the WES assay.",
"properties": {
"alignment": {
"$id": "alignment",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "WES output align files.",
"properties": {
"align_recalibrated": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_recalibrated_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"align_sorted_dedup": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_sorted_dedup_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [
"align_sorted_dedup",
"align_sorted_dedup_index"
],
"title": "WES Alignment Output Files",
"type": "object"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"germline": {
"$id": "germline",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Germline variant output sample files.",
"properties": {
"haplotyper_targets": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
}
},
"required": [
"haplotyper_targets"
],
"title": "WES Germline Output Files",
"type": "object"
},
"metrics": {
"$id": "coverage_metrics",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Coverage metrics output files.",
"properties": {
"all_summaries": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_broad": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mda": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mocha": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"coverage_metrics",
"target_metrics"
],
"title": "WES Metric Output Files",
"type": "object"
},
"optitype": {
"$id": "optitype",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "HLA output files.",
"properties": {
"optitype_result": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"xhla_report_hla": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"optitype_result"
],
"title": "WES Optitype/HLA Output Files",
"type": "object"
}
},
"required": [
"cimac_id"
],
"title": "WES sample analysis files",
"type": "object"
},
"purity": {
"$id": "purity",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Purity output files.",
"properties": {
"optimal_purity_value": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"optimal_purity_value"
],
"title": "WES Purity Output Files",
"type": "object"
},
"report": {
"$id": "report",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "WES pipeline version/commit string.",
"properties": {
"config": {
"$id": "yaml_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a YAML file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "YAML",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "YAML Artifact",
"type": "object"
},
"metasheet": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"report": {
"$id": "gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a GZ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "GZ Artifact",
"type": "object"
},
"tumor_mutational_burden": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"wes_run_version": {
"$id": "tsv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a tab Separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "TSV Artifact",
"type": "object"
},
"wes_sample_json": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
},
"wes_version": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"config",
"wes_run_version",
"metasheet",
"tumor_mutational_burden",
"report",
"wes_sample_json"
],
"title": "WES Pipeline Version",
"type": "object"
},
"run_id": {
"description": "An id used for a paired analysis run.",
"type": "string"
},
"somatic": {
"$id": "somatic",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Somatic variant calling output sample files.",
"properties": {
"maf_tnscope_filter": {
"$id": "maf_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a MAF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "MAF",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "MAF Artifact",
"type": "object"
},
"maf_tnscope_output": {
"$id": "maf_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a MAF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "MAF",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "MAF Artifact",
"type": "object"
},
"tnscope_exons": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
},
"vcf_compare": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"vcf_gz_tnscope_filter": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
},
"vcf_gz_tnscope_output": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
},
"vcf_tnscope_filter": {
"$id": "vcf_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "VCF Artifact",
"type": "object"
},
"vcf_tnscope_output": {
"$id": "vcf_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "VCF Artifact",
"type": "object"
}
},
"required": [
"vcf_gz_tnscope_output",
"vcf_gz_tnscope_filter",
"maf_tnscope_output",
"maf_tnscope_filter",
"tnscope_exons",
"vcf_compare"
],
"title": "WES Somatic Output Files",
"type": "object"
},
"tumor": {
"$id": "wes_sample_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Sample wise analysis files for the WES assay.",
"properties": {
"alignment": {
"$id": "alignment",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "WES output align files.",
"properties": {
"align_recalibrated": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_recalibrated_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"align_sorted_dedup": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_sorted_dedup_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [
"align_sorted_dedup",
"align_sorted_dedup_index"
],
"title": "WES Alignment Output Files",
"type": "object"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"germline": {
"$id": "germline",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Germline variant output sample files.",
"properties": {
"haplotyper_targets": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
}
},
"required": [
"haplotyper_targets"
],
"title": "WES Germline Output Files",
"type": "object"
},
"metrics": {
"$id": "coverage_metrics",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Coverage metrics output files.",
"properties": {
"all_summaries": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_broad": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mda": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mocha": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"coverage_metrics",
"target_metrics"
],
"title": "WES Metric Output Files",
"type": "object"
},
"optitype": {
"$id": "optitype",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "HLA output files.",
"properties": {
"optitype_result": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"xhla_report_hla": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"optitype_result"
],
"title": "WES Optitype/HLA Output Files",
"type": "object"
}
},
"required": [
"cimac_id"
],
"title": "WES sample analysis files",
"type": "object"
}
},
"required": [
"normal",
"tumor",
"run_id"
],
"title": "WES Pair Analysis Output Files",
"type": "object"
},
"mergeOptions": {
"$comment": "TODO fix to merge by a pair of normal and tumor ids. It requires improvements to the merge strategy code.",
"idRef": "/run_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"title": "WES analysis combined files",
"type": "object"
}
},
"title": "Analysis outputs for assays for this trial.",
"type": "object"
},
"assays": {
"$comment": "Assays for this trial",
"$id": "available_assays",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Reference for every available assay in network.",
"mergeStrategy": "objectMerge",
"properties": {
"cytof_10021": {
"description": "Information about the acquisition and analysis CyTOF data for 10021 and similarly formatted trials.",
"items": {
"$id": "cytof_10021",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "cytof_core",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antibody": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"entry": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
}
},
"description": "Base information about the acquisition and analysis CyTOF data.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "antibody"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cytof_antibodies",
"assay_run_id",
"batch_id"
],
"title": "CYTOF Run",
"type": "object"
}
],
"description": "Information about the acquisition and analysis CyTOF data for 10021 and similarly formatted trials.",
"mergeStrategy": "objectMerge",
"properties": {
"acquisition_buffer": {
"description": "Cell staining buffer used for antibody and cell dilution.",
"type": "string"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"astrolabe_analysis": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"astrolabe_reports": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"bead_removal": {
"description": "Boolean to indicate whether beads have been removed after normalization process",
"type": "boolean"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "antibody"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"date_of_acquisition": {
"description": "Date of CyTOF batch acquisition.",
"type": "string"
},
"debarcoding_protocol": {
"description": "The strategy/kit used to barcode CyTOF samples, if any",
"type": "string"
},
"harware_version": {
"description": "Version no. of instrument hardware used.",
"type": "string"
},
"injector": {
"description": "Name of Injector component used as part of the CyTOF software",
"type": "string"
},
"instrument": {
"description": "Name of CyTOF instrument on which experiment was conducted.",
"type": "string"
},
"normalization_method": {
"description": "Process used for normalization prior to analysis, if any.",
"enum": [
"Fluidigm",
"Other"
],
"type": "string"
},
"records": {
"description": "A single data record from CyTOF assay batch.",
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"source_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
},
"spike_in_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"assay_creator",
"batch_id",
"records"
],
"title": "CYTOF Run",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"cytof_e4412": {
"description": "Information about the acquisition and analysis CyTOF data for E4412 and similarly formatted trials.",
"items": {
"$id": "cytof_e4412",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "cytof_core",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antibody": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"entry": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
}
},
"description": "Base information about the acquisition and analysis CyTOF data.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "antibody"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cytof_antibodies",
"assay_run_id",
"batch_id"
],
"title": "CYTOF Run",
"type": "object"
}
],
"definitions": {
"participant": {
"additionalProperties": false,
"description": "A data record for a single participant from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_participant_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.Id of a participant within this clinical trial, that this assay record is based upon.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"control": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
}
},
"required": [
"input_files"
],
"type": "object"
},
"participant_debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cimac_participant_id",
"samples",
"control"
],
"type": "object"
}
},
"description": "Information about the acquisition and analysis CyTOF data for E4412 and similarly formatted trials.",
"mergeStrategy": "objectMerge",
"properties": {
"acquisition_buffer": {
"description": "Cell staining buffer used for antibody and cell dilution.",
"type": "string"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run. Not necessarily unique across batches.",
"type": "string"
},
"astrolabe_analysis": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"astrolabe_reports": {
"$id": "zip_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a ZIP file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ZIP",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ZIP Artifact",
"type": "object"
},
"batch_id": {
"description": "CyTOF batch identification number. Unique to every batch.",
"type": "string"
},
"cytof_antibodies": {
"items": {
"additionalProperties": false,
"description": "Data specific to antibody preparation on the CyTOF assay.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"isotope": {
"description": "Antibody isotype used to help differentiate antibody signals.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"stain_type": {
"description": "Type of staining method used for antibody.",
"enum": [
"Surface Stain",
"Intracellular"
],
"type": "string"
},
"usage": {
"description": "How this antibody should be used in automatic analysis",
"enum": [
"Ignored",
"Used",
"Analysis Only"
],
"type": "string"
}
},
"required": [
"isotope",
"dilution",
"stain_type",
"usage"
],
"type": "object"
},
"mergeOptions": {
"idRef": "antibody"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"debarcoding_protocol": {
"description": "The strategy/kit used to barcode CyTOF samples, if any",
"type": "string"
},
"participants": {
"items": {
"additionalProperties": false,
"description": "A data record for a single participant from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_participant_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.Id of a participant within this clinical trial, that this assay record is based upon.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"control": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
}
},
"required": [
"input_files"
],
"type": "object"
},
"participant_debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A single data record from CyTOF assay batch.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"concatenation_version": {
"description": "Concatenation of FCS files into a single FCS version number.",
"type": "string"
},
"debarcoding_key": {
"description": "An ID that maps to the specific isotope labeling scheme in the debarcoding protocol.",
"type": "string"
},
"input_files": {
"additionalProperties": false,
"description": "CyTOF Assay Input Files",
"properties": {
"intermediate_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"processed_fcs": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
}
},
"required": [
"processed_fcs"
],
"type": "object"
},
"normalization_version": {
"description": "Version of normalization for CyTOF assay batch.",
"type": "string"
},
"notes": {
"description": "Any notes pertaining to CyTOF acquisition.",
"type": "string"
},
"output_files": {
"additionalProperties": false,
"description": "Output files generated from the CyTOF assay: FCS file with enumerations for compartment, assignment and profiling cell labels; 3 CSV keys for mapping from respective enumeration indices to the cell labels; 3 CSV files providing cell count information for each of the cell labels",
"properties": {
"assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_assignment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"cell_counts_profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"compartment": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"fcs_file": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"profiling": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"preprocessing_notes": {
"description": "Any notes pertaining to preprocessing of CyTOF data.",
"type": "string"
},
"staining_date": {
"description": "Date of staining for CyTOF assay slides.",
"format": "date",
"type": "string"
}
},
"required": [
"cimac_id",
"input_files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cimac_participant_id",
"samples",
"control"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_participant_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"source_fcs": {
"items": {
"$id": "fcs_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a FCS file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FCS",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "FCS Artifact",
"type": "object"
},
"type": "array"
}
},
"required": [
"assay_creator",
"batch_id",
"participants"
],
"title": "CYTOF Run",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"elisa": {
"description": "Base information about the acquisition and analysis of ELISA data.",
"items": {
"$id": "elisa_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"definitions": {
"antigen": {
"additionalProperties": false,
"description": "Data specific to antigen preparation on the ELISA assay.",
"mergeStrategy": "objectMerge",
"properties": {
"antigen": {
"description": "Identifying name for the antigen.",
"type": "string"
},
"antigen_type": {
"description": "The type of antigen, either protein or peptide",
"enum": [
"protein",
"peptide"
],
"type": "string"
},
"final_concentration": {
"description": "The concentration of the antigen after dilution.",
"type": "number"
},
"final_concentration_units": {
"description": "The concentration units for the antigen after dilution.",
"enum": [
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Nanomolar",
"Micromolar",
"Millimolar",
"Not Reported",
"Other"
],
"type": "string"
}
},
"required": [
"antigen",
"antigen_type"
],
"type": "object"
}
},
"description": "High-throughput multiplexed assays for protein biomarker discovery.",
"mergeStrategy": "objectMerge",
"properties": {
"antigens": {
"items": {
"additionalProperties": false,
"description": "Data specific to antigen preparation on the ELISA assay.",
"mergeStrategy": "objectMerge",
"properties": {
"antigen": {
"description": "Identifying name for the antigen.",
"type": "string"
},
"antigen_type": {
"description": "The type of antigen, either protein or peptide",
"enum": [
"protein",
"peptide"
],
"type": "string"
},
"final_concentration": {
"description": "The concentration of the antigen after dilution.",
"type": "number"
},
"final_concentration_units": {
"description": "The concentration units for the antigen after dilution.",
"enum": [
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Nanomolar",
"Micromolar",
"Millimolar",
"Not Reported",
"Other"
],
"type": "string"
}
},
"required": [
"antigen",
"antigen_type"
],
"type": "object"
},
"mergeOptions": {
"idRef": "antigen"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_run_id": {
"description": "User defined unique identifier for this assay run.",
"type": "string"
},
"assay_xlsx": {
"$comment": "TODO Maybe add array of antibodies parsing.",
"$id": "artifact_elisa_xlsx",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an ELISA file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "ELISA",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "ELISA results artifact",
"type": "object"
}
},
"required": [
"assay_run_id",
"assay_xlsx",
"antigens"
],
"title": "ELISA Assay",
"type": "object"
},
"mergeOptions": {
"idRef": "assay_run_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"hande": {
"description": "H & E.",
"items": {
"$id": "hande_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"input": {
"additionalProperties": false,
"description": "H & E assay input files.",
"properties": {
"image_file": {
"$comment": "Path to the H & E image in SVS format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"image_file"
],
"type": "object"
},
"record": {
"additionalProperties": false,
"description": "A single data record from H & E assay.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "H & E assay input files.",
"properties": {
"image_file": {
"$comment": "Path to the H & E image in SVS format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"image_file"
],
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"type": "object"
}
},
"description": "H & E assay",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"records": {
"description": "A single data record from H & E assay.",
"items": {
"additionalProperties": false,
"description": "A single data record from H & E assay.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "H & E assay input files.",
"properties": {
"image_file": {
"$comment": "Path to the H & E image in SVS format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"image_file"
],
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"records",
"assay_creator"
],
"title": "H&E Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"ihc": {
"description": "Immunohistochemical analysis.",
"items": {
"$id": "ihc",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
}
],
"description": "Immunohistochemical analysis.",
"mergeStrategy": "objectMerge",
"properties": {
"antibody": {
"$id": "ihc_antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"description": "Data specific to antibody preparation for Immunohistochemical analysis.",
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilution": {
"description": "Concentration ratio for antibody dilution.",
"type": "string"
},
"incubation_temp": {
"description": "Temperature used for antibody incubation.",
"type": "string"
},
"incubation_time": {
"description": "Time duration of antibody incubation.",
"format": "time",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"dilution",
"incubation_time",
"incubation_temp"
],
"title": "IHC antibody",
"type": "object"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"autostainer_model": {
"description": "Model version of the autostainer instrument.",
"enum": [
"Bond RX",
"N/A"
],
"type": "string"
},
"records": {
"description": "A single data record from IHC assay.",
"items": {
"$id": "ihc_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"anyOf": [
{
"required": [
"tumor_proportion_score"
]
},
{
"required": [
"combined_positive_score"
]
},
{
"required": [
"inflammatory_cells"
]
},
{
"required": [
"positive_inflammatory_cell_area"
]
},
{
"required": [
"intensity"
]
},
{
"required": [
"percentage_expression"
]
},
{
"required": [
"h_score"
]
}
],
"description": "A single data record from IHC assay.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"combined_positive_score": {
"description": "Combined Positive Score (CPS) is the percentage of marker staining cells (tumor cells and cells that are non-tumor) relative to all viable tumor cells. (0-1)",
"maximum": 1,
"minimum": 0,
"type": "number"
},
"comment": {
"description": "A text comment regarding this slide.",
"type": "string"
},
"files": {
"$id": "ihc_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "IHC assay input/output files.",
"properties": {
"ihc_image": {
"$comment": "Path to IHC image in TIFF format.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"ihc_image"
],
"title": "Immunohistochemical Analysis Input Files",
"type": "object"
},
"h_score": {
"description": "A summation of the percentage of area stained at each intensity level multiplied by the weighted intensity. (0-300)",
"maximum": 300,
"minimum": 0,
"type": "integer"
},
"inflammatory_cells": {
"description": "Percentage of inflammatory cells (non-tumor cells) showing marker staining relative to all inflammatory cells. (0-1)",
"maximum": 1,
"minimum": 0,
"type": "number"
},
"intensity": {
"description": "A measure of the intensity or brightness of the protein. (0-3)",
"maximum": 3,
"minimum": 0,
"type": "number"
},
"marker_positive": {
"description": "Indicates whether the marker is considered positive by clinical trial guidelines (if applicable).",
"enum": [
"positive",
"negative",
"no_call"
],
"type": "string"
},
"percentage_expression": {
"description": "A percentage of the relevant cells considered positive. (0-100)",
"maximum": 100,
"minimum": 0,
"type": "number"
},
"positive_inflammatory_cell_area": {
"description": "Area of PD-L1+ Inflammatory Cells over the area of TSI + IT as a percentage. (0-1)",
"maximum": 1,
"minimum": 0,
"type": "number"
},
"tumor_proportion_score": {
"description": "Tumor Proportion Score (TPS) is the percentage of viable tumor cells showing marker staining relative to all viable tumor cells. (0-1)",
"maximum": 1,
"minimum": 0,
"type": "number"
}
},
"required": [
"cimac_id",
"files",
"marker_positive"
],
"title": "IHC assay record",
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
},
"staining_platform": {
"description": "Staining platform used for tissue sample labeling.",
"enum": [
"auto",
"manual"
],
"type": "string"
}
},
"required": [
"slide_scanner_model",
"staining_platform",
"autostainer_model",
"antibody",
"records"
],
"title": "IHC Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"micsss": {
"description": "Multiplexed immunohistochemical consecutive staining on single slide.",
"items": {
"$id": "micsss",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Base information about the acquisition and analysis of a quantitative pathology image.",
"inheritableBase": true,
"properties": {
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
}
},
"required": [
"slide_scanner_model"
],
"title": "Image",
"type": "object"
},
{
"$id": "imaging_data",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Shared schema for experiments involving the use of imaging data.",
"inheritableBase": true,
"properties": {
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"staining": {
"description": "'manual' or Model version of the autostainer instrument used for tissue sample labeling.",
"enum": [
"manual",
"Bond RX"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"title": "Imaging Data",
"type": "object"
}
],
"description": "Multiplexed immunohistochemical consecutive staining on single slide.",
"properties": {
"antibody": {
"items": {
"$id": "micsss_antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"description": "Data specific to antibody preparation on the multiplex immunohistochemical platform.",
"properties": {
"ar_incubation_time": {
"description": "Time of AR reagent incubation.",
"format": "time",
"type": "string"
},
"ar_ph": {
"description": "pH levels of reagents from heating antigen retrieval procedure.",
"type": "string"
},
"ar_reagent": {
"description": "Heating antigen retrieval reagents for tissue preparation.",
"type": "string"
},
"isotype": {
"description": "Antibody isotype used to help differentiate non-specific background signal from specific antibody signal.",
"type": "string"
},
"postPrimary_linker_block": {
"description": "Linker block between the antibody and the therapeutic drug.",
"type": "string"
},
"primary_antibody_block": {
"description": "Blocking reagent used for primary antibody sample.",
"type": "string"
},
"primary_antibody_dilution": {
"description": "Concentration ratio of dilution buffer for primary antibody.",
"type": "string"
},
"primary_antibody_incubation_temp": {
"description": "Temperature used for primary antibody incubation.",
"type": "string"
},
"primary_antibody_incubation_time": {
"description": "Time of primary antibody incubation.",
"format": "time",
"type": "string"
},
"secondary_antibody": {
"description": "Secondary antibody used to bind to primary antibody for detection assistance.",
"type": "string"
},
"secondary_antibody_block": {
"description": "Secondary antibody blocking reagent used for primary sample.",
"type": "string"
},
"secondary_antibody_dilution": {
"description": "Concentration ratio of dilution buffer for secondary antibody prep.",
"type": "string"
},
"secondary_antibody_incubation_time": {
"description": "Temperature used for secondary antibody incubation.",
"format": "time",
"type": "string"
},
"secondary_cat_num": {
"description": "Antibody registry catalog number assigned to secondary antibody sample.",
"type": "number"
},
"secondary_company": {
"description": "Company from which secondary antibody sample was derived.",
"type": "string"
},
"secondary_lot_num": {
"description": "Identification number assigned to the particular quantity or lot of secondary antibody material from manufacturer.",
"type": "number"
},
"species": {
"description": "Host species from which primary antibody sample was derived.",
"type": "string"
}
},
"required": [
"primary_antibody_block"
],
"title": "MICSSS antibody",
"type": "object"
},
"type": "array"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"records": {
"description": "A single data record from micsss assay.",
"items": {
"$id": "micsss_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "A single data record from micsss assay.",
"properties": {
"files": {
"$id": "micsss_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "micsss assay input files.",
"properties": {
"Composite Image Artifacts": {
"description": "Regions of interest obtained from composite images.",
"items": {
"$id": "composite_image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from composite images.",
"inheritableBase": true,
"properties": {
"component_data": {
"$comment": "Imaging data resulting from the individual components of the imaging experiment.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"composite_image": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"im3": {
"$comment": "PerkinElmer Multispectral Images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"title": "Composite Image",
"type": "object"
},
"type": "array"
},
"Mapping Artifacts": {
"description": "Regions of interest obtained from image mapping.",
"items": {
"$id": "image_mapping",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from image mapping.",
"inheritableBase": true,
"properties": {
"binary_seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped with binary values.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"cell_seg_data": {
"$comment": "Data produced from the analysis of cellular image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"cell_seg_data_summary": {
"$comment": "Summary of the results of a cell segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"score_data": {
"items": {
"$comment": "Generation of values based on experiment data.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"type": "array"
},
"seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"tissue_seg_data": {
"$comment": "Data produced from the analysis of tissue image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tissue_seg_data_summary": {
"$comment": "Summary of the results of a tissue segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"title": "Image Mapping",
"type": "object"
},
"type": "array"
},
"micsss_output_summary": {
"$comment": "Summary of the results of the experiment.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [],
"title": "Multiplexed Immunohistochemical Input Files",
"type": "object"
},
"micsss_exported_data_folder": {
"description": "Folder path containing imaging files.",
"type": "string"
},
"project_qupath_folder": {
"description": "Folder path containing files produced from a QuPath image analysis.",
"type": "string"
}
},
"required": [
"project_qupath_folder",
"micsss_exported_data_folder"
],
"title": "micsss assay record",
"type": "object"
},
"type": "array"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"required": [
"records"
],
"title": "MICSSS Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"mif": {
"description": "Multiplex immunofluorescence.",
"items": {
"$id": "mif",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Base information about the acquisition and analysis of a quantitative pathology image.",
"inheritableBase": true,
"properties": {
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
}
},
"required": [
"slide_scanner_model"
],
"title": "Image",
"type": "object"
},
{
"$id": "imaging_data",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Shared schema for experiments involving the use of imaging data.",
"inheritableBase": true,
"properties": {
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"staining": {
"description": "'manual' or Model version of the autostainer instrument used for tissue sample labeling.",
"enum": [
"manual",
"Bond RX"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"title": "Imaging Data",
"type": "object"
}
],
"description": "Multiplex immunofluorescence.",
"mergeStrategy": "objectMerge",
"properties": {
"antibodies": {
"items": {
"$id": "mif_antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "antibody",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common information about an antibody used in a number of immune-oncology assays.",
"inheritableBase": true,
"properties": {
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
}
},
"required": [
"antibody"
],
"title": "Antibody",
"type": "object"
}
],
"description": "Data specific to antibody preparation on the multiplex immunofluorescence platform.",
"mergeStrategy": "objectMerge",
"properties": {
"amplification_time": {
"description": "Length of time required for amplified signal detection.",
"format": "time",
"type": "string"
},
"antibody": {
"description": "Antibody type collected for this study.",
"type": "string"
},
"antigen_retrieval_time": {
"description": "Length of time needed for antigen retrieval.",
"format": "time",
"type": "string"
},
"cat_num": {
"description": "Antibody registry catalog number assigned to antibody sample.",
"type": "string"
},
"clone": {
"description": "Resulting type of antibody clone from primary antibody sample.",
"type": "string"
},
"company": {
"description": "Company from which antibody sample was derived.",
"type": "string"
},
"dilutent": {
"description": "Dilution agent used for antibody sample.",
"type": "string"
},
"export_name": {
"description": "Name of this antibody in InForm export, e.g. 'CD8 (Opal 520)'",
"type": "string"
},
"fluor_dilution": {
"description": "Concentration ratio for fluor dilution agent.",
"type": "string"
},
"fluor_wavelength": {
"description": "Wavelength registered for Alexa Fluor processing.",
"type": "integer"
},
"lot_num": {
"description": "Identification number assigned to the particular quantity or lot of material from manufacturer.",
"type": "string"
},
"primary_ab_dilution": {
"description": "Concentration ratio for primary antibody dilution.",
"type": "string"
},
"primary_incubation_time": {
"description": "Length of time for primary antibody incubation.",
"format": "time",
"type": "string"
},
"staining_order": {
"description": "Order of staining applied",
"type": "integer"
}
},
"required": [
"fluor_wavelength",
"primary_ab_dilution",
"dilutent",
"fluor_dilution",
"antigen_retrieval_time",
"primary_incubation_time",
"amplification_time"
],
"title": "mIF antibody",
"type": "object"
},
"mergeOptions": {
"idRef": "antibody"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"cell_segmentation_model": {
"description": "Model used for cell segmentation in an imaging experiment.",
"enum": [
"proprietary",
"watershed"
],
"type": "string"
},
"image_analysis_software": {
"description": "Source software for digital pathology and image analysis.",
"enum": [
"InForm",
"QuPath"
],
"type": "string"
},
"image_analysis_software_version": {
"description": "Source software version for digital pathology and image analysis.",
"type": "string"
},
"imaging_date": {
"description": "Date on which imaging experiment was analyzed.",
"format": "date",
"type": "string"
},
"imaging_status": {
"description": "Imaging experiment's successful completion.",
"enum": [
"Yes",
"No"
],
"type": "string"
},
"panel": {
"enum": [
"Panel 1: PD-L1, CD68, PD-1, CD8, CD3, pan-cytokeratin, DAPI",
"Panel 2: FOXP3, Granzyme B, CD45RO, CD8, CD3, pan-cytokeratin, DAPI",
"Panel 3: pan-cytokeratin, CD8, PD-1, PD-L1, DAPI",
"Panel 4: SOX10, CD8, PD-1, PD-L1, DAPI"
],
"type": "string"
},
"positive_cell_detection": {
"description": "Model used for positive cell detection in imaging experiment.",
"enum": [
"proprietary",
"random forest classifier"
],
"type": "string"
},
"records": {
"description": "A single data record from mIF assay.",
"items": {
"$id": "mif_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "A single data record from mIF assay.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$id": "mif_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "mIF assay input files.",
"properties": {
"mif_output_summary": {
"$comment": "Summary of the results of the experiment.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"regions_of_interest": {
"items": {
"$id": "mif_roi",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "composite_image",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from composite images.",
"inheritableBase": true,
"properties": {
"component_data": {
"$comment": "Imaging data resulting from the individual components of the imaging experiment.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"composite_image": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"im3": {
"$comment": "PerkinElmer Multispectral Images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"title": "Composite Image",
"type": "object"
}
],
"description": "A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.",
"mergeStrategy": "objectMerge",
"properties": {
"component_data": {
"$comment": "Imaging data resulting from the individual components of the imaging experiment.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"composite_image": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"exports": {
"items": {
"$id": "mif_export",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "image_mapping",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Regions of interest obtained from image mapping.",
"inheritableBase": true,
"properties": {
"binary_seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped with binary values.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"cell_seg_data": {
"$comment": "Data produced from the analysis of cellular image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"cell_seg_data_summary": {
"$comment": "Summary of the results of a cell segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"score_data": {
"items": {
"$comment": "Generation of values based on experiment data.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"type": "array"
},
"seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"tissue_seg_data": {
"$comment": "Data produced from the analysis of tissue image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tissue_seg_data_summary": {
"$comment": "Summary of the results of a tissue segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"title": "Image Mapping",
"type": "object"
}
],
"description": "An analysis export from inForm of a region of interest (ROI).",
"mergeOptions": {
"idRef": "/export_id"
},
"mergeStrategy": "objectMerge",
"properties": {
"binary_seg_maps": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped with binary values.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"cell_seg_data": {
"$comment": "Data produced from the analysis of cellular image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"cell_seg_data_summary": {
"$comment": "Summary of the results of a cell segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"export_id": {
"description": "Name used for an inForm export of a region of interest within one mIF slide, e.g. CD8, CD45RO",
"type": "string"
},
"image_with_all_seg": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"image_with_cell_seg_map": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"image_with_phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"image_with_tissue_seg": {
"$comment": "Results of a computer vision task, in which specific regions of a region are mapped.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"phenotype_map": {
"$comment": "Image produced from the combination of multiple imaging experiment data images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"score_data": {
"items": {
"$comment": "Generation of values based on experiment data.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"type": "array"
},
"tissue_seg_data": {
"$comment": "Data produced from the analysis of tissue image.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"tissue_seg_data_summary": {
"$comment": "Summary of the results of a tissue segmentation data experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"export_id",
"cell_seg_data",
"cell_seg_data_summary"
]
},
"mergeOptions": {
"idRef": "/export_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"im3": {
"$comment": "PerkinElmer Multispectral Images.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"roi_id": {
"description": "Identifier of a region of interest within one mIF slide, e.g. 1, 2, 3 or [123 x 321]",
"type": "string"
}
},
"required": [
"roi_id",
"exports"
]
},
"mergeOptions": {
"idRef": "/roi_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"roi_annotations": {
"$comment": "Text describing region of interest for experiment.",
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"whole_slide_imaging_file": {
"$comment": "Digital slide produced from the scanning of conventional glass slides.",
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
}
},
"required": [
"regions_of_interest"
],
"title": "Multiplex Immunofluorescence Input Files",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "mIF assay record",
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"slide_scanner_model": {
"description": "Model version of the slide scanner instrument.",
"enum": [
"Vectra 2.0",
"Hamamatsu"
],
"type": "string"
},
"staining": {
"description": "'manual' or Model version of the autostainer instrument used for tissue sample labeling.",
"enum": [
"manual",
"Bond RX"
],
"type": "string"
},
"staining_date": {
"description": "Date on which slide staining was processed.",
"format": "date",
"type": "string"
}
},
"required": [
"records",
"panel",
"antibodies"
],
"title": "mIF Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"nanostring": {
"description": "Nanostring",
"items": {
"$id": "nanostring_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"run": {
"additionalProperties": false,
"description": "A single Nanostring run.",
"properties": {
"control_raw_rcc": {
"$comment": "The RCC data file for a reference RNA sample",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
},
"run_id": {
"description": "A unique ID that separates the different runs of the given same sample.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A data record for a single sample from a single Nanostring run.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"raw_rcc": {
"$comment": "The RCC data file generated by Nanostring for the given sample in the given run.",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
}
},
"required": [
"cimac_id",
"raw_rcc"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"run_id",
"samples"
],
"type": "object"
},
"sample": {
"additionalProperties": false,
"description": "A data record for a single sample from a single Nanostring run.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"raw_rcc": {
"$comment": "The RCC data file generated by Nanostring for the given sample in the given run.",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
}
},
"required": [
"cimac_id",
"raw_rcc"
],
"type": "object"
}
},
"description": "A microarray assay for expression levels, suitable for smaller samples than RNA-seq",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"batch_id": {
"description": "A unique ID that separates the different batches of Nanostring.",
"type": "string"
},
"data": {
"additionalProperties": false,
"properties": {
"normalized": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"raw": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"type": "object"
},
"runs": {
"items": {
"additionalProperties": false,
"description": "A single Nanostring run.",
"properties": {
"control_raw_rcc": {
"$comment": "The RCC data file for a reference RNA sample",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
},
"run_id": {
"description": "A unique ID that separates the different runs of the given same sample.",
"type": "string"
},
"samples": {
"items": {
"additionalProperties": false,
"description": "A data record for a single sample from a single Nanostring run.",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"raw_rcc": {
"$comment": "The RCC data file generated by Nanostring for the given sample in the given run.",
"$id": "rcc_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Nanostring output file. XML-formatted comma-separated tables",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "RCC",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "RCC Artifact",
"type": "object"
}
},
"required": [
"cimac_id",
"raw_rcc"
],
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"run_id",
"samples"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/run_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"data",
"runs"
],
"title": "Nanostring Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"olink": {
"$comment": "NB This is not array as every other assay. Will update data on any olink upload.",
"$id": "olink_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"batch": {
"additionalProperties": false,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_panel_lot": {
"description": "Lot number of the assay panel.",
"type": "string"
},
"batch_id": {
"description": "A unique identifier for this Olink upload",
"type": "string"
},
"combined": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
},
"panel": {
"description": "Panel used for the assay.",
"type": "string"
},
"records": {
"description": "A single data record from Olink assay.",
"items": {
"additionalProperties": false,
"description": "A single data record from Olink assay.",
"properties": {
"baseline_correction": {
"description": "Method used for baseline correction.",
"type": "string"
},
"chip_barcode": {
"description": "Chip barcode number.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"fludigm_application_build": {
"description": "Build of the Fluidgm application used.",
"type": "string"
},
"fludigm_application_version": {
"description": "Version of the Fluidgm application used.",
"type": "string"
},
"instrument": {
"description": "Instrument used for the Olink assay.",
"type": "string"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples analyzed in the assay.",
"type": "number"
},
"number_of_samples_failed": {
"description": "Number of samples failed in the assay.",
"type": "number"
},
"passive_reference": {
"description": "Passive Reference.",
"type": "string"
},
"probe_type": {
"description": "Probe Type.",
"type": "string"
},
"quality_threshold": {
"description": "Threshold used for quality cutoff.",
"type": "number"
},
"run_date": {
"description": "Date when the Olink assay was run.",
"format": "date",
"type": "string"
},
"run_time": {
"description": "Time when the Olink assay was run.",
"format": "time",
"type": "string"
}
},
"required": [
"number_of_samples",
"npx_manager_version",
"files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/chip_barcode"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"batch_id",
"panel",
"records",
"assay_creator"
],
"type": "object"
},
"combined_npx": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
},
"input": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"record": {
"additionalProperties": false,
"description": "A single data record from Olink assay.",
"properties": {
"baseline_correction": {
"description": "Method used for baseline correction.",
"type": "string"
},
"chip_barcode": {
"description": "Chip barcode number.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"fludigm_application_build": {
"description": "Build of the Fluidgm application used.",
"type": "string"
},
"fludigm_application_version": {
"description": "Version of the Fluidgm application used.",
"type": "string"
},
"instrument": {
"description": "Instrument used for the Olink assay.",
"type": "string"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples analyzed in the assay.",
"type": "number"
},
"number_of_samples_failed": {
"description": "Number of samples failed in the assay.",
"type": "number"
},
"passive_reference": {
"description": "Passive Reference.",
"type": "string"
},
"probe_type": {
"description": "Probe Type.",
"type": "string"
},
"quality_threshold": {
"description": "Threshold used for quality cutoff.",
"type": "number"
},
"run_date": {
"description": "Date when the Olink assay was run.",
"format": "date",
"type": "string"
},
"run_time": {
"description": "Time when the Olink assay was run.",
"format": "time",
"type": "string"
}
},
"required": [
"number_of_samples",
"npx_manager_version",
"files"
],
"type": "object"
}
},
"description": "High-throughput multiplexed assays for protein biomarker discovery.",
"mergeStrategy": "objectMerge",
"properties": {
"batches": {
"items": {
"additionalProperties": false,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"assay_panel_lot": {
"description": "Lot number of the assay panel.",
"type": "string"
},
"batch_id": {
"description": "A unique identifier for this Olink upload",
"type": "string"
},
"combined": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
},
"panel": {
"description": "Panel used for the assay.",
"type": "string"
},
"records": {
"description": "A single data record from Olink assay.",
"items": {
"additionalProperties": false,
"description": "A single data record from Olink assay.",
"properties": {
"baseline_correction": {
"description": "Method used for baseline correction.",
"type": "string"
},
"chip_barcode": {
"description": "Chip barcode number.",
"type": "string"
},
"files": {
"additionalProperties": false,
"description": "Olink assay input files.",
"properties": {
"assay_npx": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"assay_raw_ct": {
"$comment": "Number of cycles required for the fluorescent signal to cross the threshold.",
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
}
},
"required": [
"assay_npx",
"assay_raw_ct"
],
"type": "object"
},
"fludigm_application_build": {
"description": "Build of the Fluidgm application used.",
"type": "string"
},
"fludigm_application_version": {
"description": "Version of the Fluidgm application used.",
"type": "string"
},
"instrument": {
"description": "Instrument used for the Olink assay.",
"type": "string"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples analyzed in the assay.",
"type": "number"
},
"number_of_samples_failed": {
"description": "Number of samples failed in the assay.",
"type": "number"
},
"passive_reference": {
"description": "Passive Reference.",
"type": "string"
},
"probe_type": {
"description": "Probe Type.",
"type": "string"
},
"quality_threshold": {
"description": "Threshold used for quality cutoff.",
"type": "number"
},
"run_date": {
"description": "Date when the Olink assay was run.",
"format": "date",
"type": "string"
},
"run_time": {
"description": "Time when the Olink assay was run.",
"format": "time",
"type": "string"
}
},
"required": [
"number_of_samples",
"npx_manager_version",
"files"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/chip_barcode"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"batch_id",
"panel",
"records",
"assay_creator"
],
"type": "object"
},
"mergeOptions": {
"idRef": "/batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"study": {
"additionalProperties": false,
"mergeStrategy": "objectMerge",
"properties": {
"npx_file": {
"$comment": "Normalized Protein eXpression is Olink\u2019s arbitrary unit which is in Log2 scale.",
"$id": "npx_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_samples",
"samples"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an NPX file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "NPX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_samples": {
"description": "Number of samples within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"samples": {
"description": "Ids of the sample(s) within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Ids of the sample(s) within this file.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "NPX Artifact",
"type": "object"
},
"npx_manager_version": {
"description": "Version of NPX manager used for the analysis.",
"type": "string"
}
},
"required": [
"npx_manager_version",
"npx_file"
],
"type": "object"
}
},
"required": [
"batches"
],
"title": "Olink Assay",
"type": "object"
},
"rna": {
"description": "RNA assay for expression analysis.",
"items": {
"$id": "rna_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"$id": "rna_assay-v0",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "ngs_assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common properties for NGS Assays.",
"inheritableBase": true,
"properties": {
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"sequencer_platform"
],
"title": "NGS Assay Core",
"type": "object"
}
],
"description": "Additional properties to describe a RNA assay for expression analysis.",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"enrichment_method": {
"description": "Method used for enriching for mRNA.",
"enum": [
"PolyA capture",
"Transcriptome capture v1",
"Ribo minus"
],
"type": "string"
},
"enrichment_vendor_kit": {
"description": "Vendor for the bait set used for enrichment, e.g. Twist, Agilent, IDT.",
"enum": [
"Agilent",
"Twist",
"IDT",
"NEB",
"Illumina - TruSeq Stranded PolyA mRNA",
"Illumina - TruSeq Stranded mRNA Sample Prep Kit",
"Illumina- TruSeq RNA Access Library Prep Kit"
],
"type": "string"
},
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"records": {
"description": "A single data record from RNAseq assay.",
"items": {
"additionalProperties": false,
"allOf": [
{
"$id": "ngs_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A single data record from an NGS assay.",
"inheritableBase": true,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "NGS assay record",
"type": "object"
}
],
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"dv200": {
"description": "The percentage of fragments > 200 nucleotides.",
"maximum": 1,
"minimum": 0,
"type": "number"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
},
"library_yield_ng": {
"description": "Resulting yield (in ng) from library construction.",
"type": "number"
},
"quality_flag": {
"description": "Flag used for quality.",
"type": "number"
},
"rin": {
"description": "RNA integrity number. (0-10)",
"maximum": 10,
"minimum": 0,
"type": "number"
},
"rqs": {
"description": "RNA quality score. (0-10)",
"maximum": 10,
"minimum": 0,
"type": "number"
}
},
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"enrichment_method",
"records"
],
"title": "RNA Gene Expression Assay version 0",
"type": "object"
}
],
"description": "An RNA assay for expression analysis.",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"title": "RNA Gene Expression Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"tcr": {
"description": "TCR sequencing assay.",
"items": {
"$id": "tcr_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "ngs_assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common properties for NGS Assays.",
"inheritableBase": true,
"properties": {
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"sequencer_platform"
],
"title": "NGS Assay Core",
"type": "object"
}
],
"description": "Additional properties to describe a TCR assay for expression analysis.",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"batch_id": {
"description": "TCRseq batch identification number.",
"type": "string"
},
"records": {
"description": "A single data record from TCRseq assay.",
"items": {
"$id": "tcr_entry",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "A single data record from TCRseq assay.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$id": "tcr_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "TCRseq assay input files.",
"properties": {
"replicates": {
"items": {
"$id": "tcr_input",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "reads_with_index",
"$schema": "metaschema/strict_meta_schema.json#",
"allOf": [
{
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
],
"description": "Index files associated with read files, in fastq.gz format",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"i1": {
"items": {
"$comment": "Fastq file for the first index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"i2": {
"items": {
"$comment": "Fastq file for the second index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
}
},
"required": [
"i1",
"i2"
],
"title": "Reads with index",
"type": "object"
}
],
"description": "TCRseq replicate of interest.",
"mergeStrategy": "objectMerge",
"properties": {
"i1": {
"items": {
"$comment": "Fastq file for the first index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"i2": {
"items": {
"$comment": "Fastq file for the second index.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"replicate_id": {
"description": "Replicate identifier.",
"type": "string"
},
"rna_quantity_ng": {
"description": "RNA quantity (in ng).",
"type": "number"
}
},
"required": [
"replicate_id"
]
},
"mergeOptions": {
"idRef": "/replicate_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"title": "TCRseq assay Input Files",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "TCRseq assay record",
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"sample_sheet": {
"$id": "csv_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a comma separated file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "CSV",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "CSV Artifact",
"type": "object"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
},
"sequencing_run_date": {
"description": "Date when the TCR sequencing was run.",
"format": "date",
"type": "string"
}
},
"required": [
"records",
"batch_id",
"sequencing_run_date",
"sample_sheet"
],
"title": "TCR Assay",
"type": "object"
},
"mergeOptions": {
"idRef": "batch_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"wes": {
"description": "Whole exome sequencing.",
"items": {
"$id": "wes_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Main properties of the assay experiment template.",
"inheritableBase": true,
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
}
},
"required": [
"assay_creator"
],
"title": "Assay Core",
"type": "object"
},
{
"$id": "ngs_assay_core",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "Common properties for NGS Assays.",
"inheritableBase": true,
"properties": {
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
}
},
"required": [
"sequencer_platform"
],
"title": "NGS Assay Core",
"type": "object"
}
],
"description": "Whole exome sequencing.",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"bait_set": {
"description": "Bait set ID.",
"enum": [
"whole_exome_illumina_coding_v1",
"broad_custom_exome_v1",
"TWIST Dana Farber Custom Panel"
],
"type": "string"
},
"library_kit": {
"$comment": "This is 'required', but we have only one enum option here. This is incomplete as the RNAseq harmonization is still ongoing.",
"description": "The library construction kit.",
"enum": [
"Hyper Prep ICE Exome Express: 1.0",
"KAPA HyperPrep",
"IDT duplex UMI adapters",
"TWIST"
],
"type": "string"
},
"paired_end_reads": {
"description": "Indicates if the sequencing was performed paired or single ended.",
"enum": [
"Paired",
"Single"
],
"type": "string"
},
"read_length": {
"description": "Number of cycles for each sequencing read.",
"exclusiveMinimum": 0,
"maximum": 1000,
"type": "integer"
},
"records": {
"description": "A single data record from WES assay.",
"items": {
"$id": "wes_entry",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "ngs_assay_record",
"$schema": "metaschema/strict_meta_schema.json#",
"description": "A single data record from an NGS assay.",
"inheritableBase": true,
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
}
},
"required": [
"cimac_id",
"files"
],
"title": "NGS assay record",
"type": "object"
}
],
"description": "A single data record from WES assay.",
"mergeStrategy": "objectMerge",
"properties": {
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of an sample within this clinical trial, that this assay record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"files": {
"$comment": "Fastq files or a bam file produced by the assay.",
"$id": "fastq_pair_or_bam",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"r1",
"r2"
]
},
{
"required": [
"bam"
]
}
],
"description": "Paired end sequencing in a .fastq file pair or in a .bam",
"inheritableBase": true,
"mergeStrategy": "objectMerge",
"properties": {
"bam": {
"items": {
"$comment": "A BAM file, aligned or not, which contains both pairs of sequencing libraries",
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r1": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
},
"r2": {
"items": {
"$comment": "Fastq file for the first fragment.",
"$id": "artifact_fastq_gz",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped FASTQ file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "FASTQ.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped FastQ Artifact",
"type": "object"
},
"minItems": 1,
"type": "array"
}
},
"title": "Fastq pair or a bam",
"type": "object"
},
"output_files": {
"$id": "wes_sample_analysis",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Sample wise analysis files for the WES assay.",
"properties": {
"alignment": {
"$id": "alignment",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "WES output align files.",
"properties": {
"align_recalibrated": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_recalibrated_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
},
"align_sorted_dedup": {
"$id": "bam_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a BAM file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM Artifact",
"type": "object"
},
"align_sorted_dedup_index": {
"$id": "bam_bai_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Bam index file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "BAM.BAI",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "BAM.BAI Artifact",
"type": "object"
}
},
"required": [
"align_sorted_dedup",
"align_sorted_dedup_index"
],
"title": "WES Alignment Output Files",
"type": "object"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.Id of a sample within this clinical trial, that this record is based upon.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"germline": {
"$id": "germline",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Germline variant output sample files.",
"properties": {
"haplotyper_targets": {
"$id": "vcf_gz_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a Gzipped VCF file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "VCF.GZ",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Gzipped VCF Artifact",
"type": "object"
}
},
"required": [
"haplotyper_targets"
],
"title": "WES Germline Output Files",
"type": "object"
},
"metrics": {
"$id": "coverage_metrics",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Coverage metrics output files.",
"properties": {
"all_summaries": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"coverage_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_broad": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mda": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"mosdepth_region_dist_mocha": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"target_metrics_summary": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
}
},
"required": [
"coverage_metrics",
"target_metrics"
],
"title": "WES Metric Output Files",
"type": "object"
},
"optitype": {
"$id": "optitype",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "HLA output files.",
"properties": {
"optitype_result": {
"$id": "text_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a text file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "TEXT",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Text Artifact",
"type": "object"
},
"xhla_report_hla": {
"$id": "json_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"description": "Information about a JSON file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "JSON",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "JSON Artifact",
"type": "object"
}
},
"required": [
"optitype_result"
],
"title": "WES Optitype/HLA Output Files",
"type": "object"
}
},
"required": [
"cimac_id"
],
"title": "WES sample analysis files",
"type": "object"
},
"quality_flag": {
"description": "Flag used for quality.",
"type": "number"
},
"sequencing_date": {
"description": "Date of sequencing.",
"format": "date",
"type": "string"
}
},
"title": "WES assay record",
"type": "object"
},
"mergeOptions": {
"idRef": "cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"sequencer_platform": {
"description": "Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.",
"enum": [
"Illumina - HiSeq 2500",
"Illumina - HiSeq 3000",
"Illumina - NextSeq 550",
"Illumina - HiSeq 4000",
"Illumina - NovaSeq 6000",
"MiSeq"
],
"type": "string"
},
"sequencing_protocol": {
"description": "Protocol and version used for the sequencing.",
"enum": [
"Express Somatic Human WES (Deep Coverage) v1.1",
"Somatic Human WES v6"
],
"type": "string"
}
},
"required": [
"records",
"bait_set",
"read_length"
],
"title": "Whole Exome Sequencing Assay",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
}
},
"title": "Assays which are available in the network",
"type": "object"
},
"biobank": {
"description": "The primary organization responsible for storing biospecimens from this study.",
"type": "string"
},
"biomarker_plan": {
"description": "A description of the objectives and hypotheses for the proposed biomarkers.",
"type": "string"
},
"clinical_data": {
"$id": "clinical_assay",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"record": {
"additionalProperties": false,
"description": "A single data record from Clinical Data assay.",
"properties": {
"clinical_file": {
"$comment": "Path to clinical data XLSX file.",
"$id": "artifact_clinical_xlsx",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_participants",
"participants"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "A file containing clinical information.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "XLSX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_participants": {
"description": "Number of participants within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"participants": {
"description": "Ids of the participants within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.Ids of the participants within this file.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Generic clinical data artifact",
"type": "object"
},
"comment": {
"description": "A text comment regarding this file.",
"type": "string"
}
},
"required": [
"clinical_file"
],
"type": "object"
}
},
"description": "Clinical data recorded for a clinical trial",
"mergeStrategy": "objectMerge",
"properties": {
"assay_creator": {
"description": "Indicates what site is filling out the assay.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"records": {
"description": "A single file from clinical data upload.",
"items": {
"additionalProperties": false,
"description": "A single data record from Clinical Data assay.",
"properties": {
"clinical_file": {
"$comment": "Path to clinical data XLSX file.",
"$id": "artifact_clinical_xlsx",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"number_of_participants",
"participants"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "A file containing clinical information.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "XLSX",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"number_of_participants": {
"description": "Number of participants within this file.",
"type": "integer"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"participants": {
"description": "Ids of the participants within this file.",
"items": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.Ids of the participants within this file.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"type": "array"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Generic clinical data artifact",
"type": "object"
},
"comment": {
"description": "A text comment regarding this file.",
"type": "string"
}
},
"required": [
"clinical_file"
],
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
}
},
"required": [
"assay_creator",
"records"
],
"title": "Clinical Data Assay",
"type": "object"
},
"collection_event_list": {
"description": "A list associating collection events with allowed sample types.",
"items": {
"$id": "collection_event.json",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"definitions": {
"specimen_type": {
"additionalProperties": false,
"properties": {
"comments": {
"type": "string"
},
"derivatives": {
"$comment": "The derivate specimen types for this specimen type (e.g., plasma is derived from whole blood).",
"items": {
"$ref": "#/definitions/specimen_type"
},
"type": "array"
},
"intended_assays": {
"$comment": "The assay(s) with which this biospecimen will be analyzed.",
"items": {
"type": "string"
},
"type": "array"
},
"specimen_type": {
"$comment": "The name of this specimen type",
"type": "string"
}
},
"required": [
"specimen_type"
],
"type": "object"
}
},
"description": "Defines a collection event and its biospecimen type hierarchy.",
"properties": {
"event_name": {
"$comment": "The name of this collection event",
"type": "string"
},
"specimen_types": {
"$comment": "The array of root specimen types associated with this collection event",
"items": {
"$ref": "#/definitions/specimen_type"
},
"type": "array"
}
},
"type": "object"
},
"type": "array"
},
"data_sharing_plan": {
"description": "A description of the rules governing data sharing and publications.",
"type": "string"
},
"grant_or_affiliated_network": {
"description": "The primary organization providing grant funding and supporting the trial.",
"type": "string"
},
"justification": {
"description": "A description of the reasons why this study could provide insight into molecular biomarkers of immunotherapy.",
"type": "string"
},
"lead_cimac_contacts": {
"description": "A list of contacts for this trial.",
"items": {
"type": "string"
},
"type": "array"
},
"lead_cimac_pis": {
"description": "The PI(s) from the CIMAC-CIDC network responsible for this study.",
"items": {
"type": "string"
},
"type": "array"
},
"lead_trial_staff": {
"description": "The names of lead trial staff members other than the PIs.",
"items": {
"type": "string"
},
"type": "array"
},
"nci_id": {
"description": "NCI Trial Identifier. Example: NCI22345.",
"type": "string"
},
"nct_id": {
"description": "ClinicalTrials.gov identifier. Example: NCT03731260.",
"type": "string"
},
"participants": {
"description": "The collection of all data related to a specific participant in the context of a specific clinical trial.",
"items": {
"$id": "participant",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "The collection of all data related to a specific participant in the context of a specific clinical trial.\n",
"properties": {
"cidc_participant_id": {
"description": "The generated, CIDC-internal identifier for this participant.",
"example": "CIDC-Trial101-e1b2c3",
"in_doc_ref_pattern": "/participants/*/cidc_participant_id",
"pattern": "^CIDC-\\w+-\\w+$",
"type": "string"
},
"cimac_participant_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_participant_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_participant_id $ref.",
"description": "Participant identifier assigned by the CIMAC-CIDC Network. Formated as: C?????? (first 7 characters of CIMAC ID)",
"example": "CTTTP01",
"in_doc_ref_pattern": "/participants/*/cimac_participant_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}$",
"type": "string"
},
"clinical": {
"$comment": "holds whatever non-harmonized annotations trial team provides",
"additionalProperties": true,
"type": "object"
},
"cohort_name": {
"$comment": "Values in this field are validated dynamically by `in_doc_ref_pattern`.",
"description": "Categorical description of cohorts, arms, and treatment groups.",
"example": "Arm_Z",
"in_doc_ref_pattern": "/allowed_cohort_names/*",
"type": "string"
},
"essential_patient_entry_number": {
"$comment": "Used to provide id for patient entry in a shipment manifest, left here for back-compat.",
"description": "Deprecated",
"type": "integer"
},
"ethnicity": {
"description": "'NIH Racial and Ethnic Categories and Definitions for NIH Diversity Programs and for Other Reporting Purposes (NOT-OD-15-089), Release Date: April 8, 2015.'\n",
"enum": [
"Hispanic or Latino",
"Not Hispanic or Latino",
"Not reported",
"Unknown",
"Other"
],
"type": "string"
},
"gender": {
"description": "Identifies the gender of the participant.",
"enum": [
"Male",
"Female",
"Not Specified",
"Other"
],
"type": "string"
},
"participant_id": {
"description": "Trial Participant Identifier. Crypto-hashed after upload.",
"encrypt": true,
"type": "string"
},
"race": {
"description": "'NIH Racial and Ethnic Categories and Definitions for NIH Diversity Programs and for Other Reporting Purposes (NOT-OD-15-089), Release Date: April 8, 2015.'\n",
"enum": [
"American Indian/Alaska Native",
"Asian",
"Black/African American",
"Native Hawaiian/Pacific Islander",
"White",
"Not Reported",
"Unknown",
"Other"
],
"type": "string"
},
"samples": {
"items": {
"$id": "sample",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products.",
"if": {
"properties": {
"type_of_sample": {
"enum": [
"Blood"
]
}
}
},
"properties": {
"a260_a230": {
"description": "Provides an absorbance percentage ratio indicating presence of contaminants (values of 0 to 3)",
"type": "number"
},
"a260_a280": {
"description": "Provides an absorbance percentage ratio indicating purity of DNA (values of 0 to 2)",
"type": "number"
},
"aliquots": {
"description": "Pertaining to a portion (volume or weight) of the whole.",
"items": {
"$id": "aliquot",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Pertaining to a portion (volume or weight) of the whole.",
"properties": {
"aliquot_amount": {
"$comment": "RECHECK Should this be moved to the sample level or renamed?",
"description": "The amount of extracted aliquot shipped. Example: 400 ng",
"type": "string"
},
"aliquot_replacement": {
"description": "Status of aliquot if replacement is/was requested.",
"enum": [
"Replacement Requested",
"Replacement Tested",
"N/A"
],
"type": "string"
},
"aliquot_status": {
"description": "Status of aliquot used for other assay, exhausted, destroyed, or returned.",
"enum": [
"Aliquot Returned",
"Aliquot Exhausted",
"Remainder used for other Assay",
"Other",
"Aliquot Leftover"
],
"type": "string"
},
"extracted_concentration": {
"description": "The concentration of biological material that was extracted from this aliquot.",
"type": "string"
},
"lymphocyte_influx": {
"description": "Extent of lymphocytic infiltration into the tumor stroma or surrounding environment. Example: 2",
"type": "string"
},
"material_extracted": {
"description": "The type of biological material that was extracted from this aliquot.",
"enum": [
"DNA",
"RNA",
"cfDNA",
"Other"
],
"type": "string"
},
"quantity": {
"description": "Quantity of each aliquot shipped.",
"type": "integer"
},
"slide_number": {
"description": "Two digit number that indicates the sequential order of slide cuts, assigned by the CIMAC-CIDC Network.",
"pattern": "^[0-9]{1,2}$",
"type": "string"
}
},
"required": [
"slide_number",
"aliquot_replacement",
"aliquot_status"
],
"title": "Aliquot",
"type": "object"
},
"mergeOptions": {
"idRef": "/slide_number"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"box_number": {
"description": "Identifier if sample shipment container includes multiple boxes for each assay.",
"type": "string"
},
"cidc_id": {
"$comment": "in_doc_ref_pattern: /participants/*/samples/*/cidc_id",
"description": "The generated, CIDC-internal identifier for this sample.",
"example": "CIDC-Trial101-e1b2c3-a7b",
"pattern": "^CIDC-\\w+-\\w+-\\w+$",
"type": "string"
},
"cimac_id": {
"$comment": "With `in_doc_ref_pattern` here, there's no need to specify it each time cimac_id is $ref'ed, constrain will be pulled in place by ref resolver automatically, assuring that it will be checked for every cimac_id $ref.",
"description": "Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as C????????.??",
"example": "CTTTP01A1.00",
"in_doc_ref_pattern": "/participants/*/samples/*/cimac_id",
"pattern": "^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$",
"type": "string"
},
"clinical_report_id": {
"description": "A unique identifier so someone can find the clinical report.",
"encrypt": true,
"type": "string"
},
"collection_event_name": {
"$comment": "Values in this field are validated dynamically by `in_doc_ref_pattern`.",
"description": "Categorical description of timepoint at which the sample was taken.",
"in_doc_ref_pattern": "/allowed_collection_event_names/*",
"title": "Collection Event Name",
"type": "string"
},
"comments": {
"description": "Comments on sample testing.",
"type": "string"
},
"core_number": {
"description": "The biopsy core number from which the sample was used.",
"type": "number"
},
"diagnosis_verification": {
"description": "Indicates whether the local pathology review was consistent with the diagnostic pathology report.",
"enum": [
"Local pathology review was not consistent",
"Local pathology review was consistent with site of tissue procurement diagnostic pathology report",
"Not Available",
"Not Reported",
"Other"
],
"title": "Diagnosis verification",
"type": "string"
},
"din": {
"description": "Provides a DNA Integrity Number as an indication of extraction quality (values of 1-10)",
"type": "number"
},
"fibrosis_area_percentage": {
"description": "Score the percentage area of Fibrosis",
"maximum": 100,
"minimum": 0,
"type": "number"
},
"fixation_stabilization_type": {
"description": "Type of specimen fixation or stabilization that was employed by the site directly after collection.",
"enum": [
"Archival FFPE",
"Fresh Specimen",
"Frozen Specimen",
"Formalin-Fixed Paraffin-Embedded",
"Optimum cutting temperature medium",
"Thaw-Lyse",
"Not Reported",
"Other"
],
"type": "string"
},
"histology_behavior": {
"description": "ICD-0-3 code for histology and behavior. e.g. 9665/3",
"type": "string"
},
"histology_behavior_description": {
"description": "ICD-0-3 histology and behavior code description. e.g. Hodgkin lymphoma, nod. scler., grade 1",
"type": "string"
},
"intended_assay": {
"description": "The assay that this sample is expected to be used as input for.",
"type": "string"
},
"material_remaining": {
"description": "Receiving site indicates how much material remains after assay use.",
"type": "number"
},
"material_remaining_units": {
"description": "Units for the amount of material remaining.",
"enum": [
"Microliters",
"Milliliters",
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Cells per Vial",
"Slides",
"Not Reported",
"Other"
],
"type": "string"
},
"material_storage_condition": {
"description": "Storage condition of the material once it was received.",
"enum": [
"RT",
"4oC",
"(-20)oC",
"(-80)oC",
"LN",
"Not Reported",
"Other"
],
"type": "string"
},
"material_used": {
"description": "Receiving site indicates how much material was used for assay purposes.",
"type": "number"
},
"material_used_units": {
"description": "Units for the amount of material used; should be the same value as Specimen Analyte units.",
"enum": [
"Microliters",
"Milliliters",
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Cells per Vial",
"Slides",
"Not Reported",
"Other"
],
"type": "string"
},
"necrosis_area_percentage": {
"description": "Score the percentage area of necrosis",
"maximum": 100,
"minimum": 0,
"type": "number"
},
"parent_sample_id": {
"description": "Sample identifier assigned by the biorepository site. Crypto-hashed after upload.",
"encrypt": true,
"type": "string"
},
"pbmc_recovery": {
"description": "Receiving site determines number for PBMCs per vial recovered upon receipt.",
"type": "number"
},
"pbmc_resting_period_used": {
"description": "Receiving site indicates if a resting period was used after PBMC recovery.",
"enum": [
"Yes",
"No",
"Not Reported",
"Other"
],
"type": "string"
},
"pbmc_viability": {
"description": "Receiving site determines the percent recovered cells that are viable after thawing.",
"type": "number"
},
"processed_sample_concentration": {
"description": "The concentration of the processed sample.",
"type": "number"
},
"processed_sample_concentration_units": {
"description": "The concentration units for the processed sample.",
"enum": [
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Cells per Vial",
"Not Reported",
"Other"
],
"type": "string"
},
"processed_sample_derivative": {
"description": "The type of derivative or analyte extracted from the specimen to be shipped for testing.",
"enum": [
"Tumor DNA",
"Tumor RNA",
"Germline DNA",
"Circulating Tumor-Derived DNA",
"Not Reported",
"Other"
],
"type": "string"
},
"processed_sample_id": {
"description": "Aliquot identifier assigned by the biorepository site. Crypto-hashed after upload.",
"encrypt": true,
"type": "string"
},
"processed_sample_quantity": {
"description": "Quantity of the processed sample (e.g. number of slides cut for DNA extraction).",
"type": "number"
},
"processed_sample_type": {
"description": "The type of processing that was performed on the collected specimen by the Biobank for storage.",
"enum": [
"Whole Blood",
"Plasma",
"PBMC",
"Buffy Coat",
"Bone Marrow Mononuclear Cell",
"Supernatant",
"Cell Pellet",
"H&E-Stained Fixed Tissue Slide Specimen",
"Fixed Slide",
"Tissue Scroll",
"FFPE Punch",
"Not Reported",
"Other"
],
"type": "string"
},
"processed_sample_volume": {
"description": "Volume of the processed sample.",
"type": "number"
},
"processed_sample_volume_units": {
"description": "Volume units of each processed sample.",
"enum": [
"Microliters",
"Milliliters",
"Not Reported",
"Other"
],
"type": "string"
},
"quality_of_sample": {
"description": "Final status of sample after QC and pathology review.",
"enum": [
"Pass",
"Fail",
"Not Reported",
"Other"
],
"type": "string"
},
"residual_sample_use": {
"description": "Indication if sample was sent to another location or returned back to biorepository.",
"enum": [
"Sample Returned",
"Sample Sent to Another Lab",
"Sample received from CIMAC",
"Not Reported",
"Other"
],
"type": "string"
},
"sample_collection_procedure": {
"description": "Indicates the specimen source of the sample shipped. Example: Na Heparin blood draw aliquots (2 of three), FFPE block #52",
"enum": [
"Blood Draw",
"Excision",
"Core Biopsy",
"Punch Biopsy",
"Endoscopic Biopsy",
"Bone Marrow Core Biopsy",
"Bone Marrow Aspirate",
"Lumbar Puncture",
"Aspirate",
"Fine-Needle Aspiration",
"Not Reported",
"Other"
],
"type": "string"
},
"sample_derivative_concentration": {
"description": "The concentration of analyte or derivative shipped.",
"type": "number"
},
"sample_derivative_concentration_units": {
"description": "The concentration units for the analyte or derivative shipped.",
"enum": [
"Nanogram per Microliter",
"Milligram per Milliliter",
"Micrograms per Microliter",
"Cells per Vial",
"Not Reported",
"Other"
],
"type": "string"
},
"sample_derivative_volume": {
"description": "Volume of the analyte or derivative shipped.",
"type": "number"
},
"sample_derivative_volume_units": {
"description": "Volume units of each analyte or derivative shipped.",
"enum": [
"Microliters",
"Milliliters",
"Not Reported",
"Other"
],
"type": "string"
},
"sample_location": {
"description": "Sample location within the shipping container. Example: A1.",
"type": "string"
},
"sample_replacement": {
"description": "Indication if sample replacement is/was requested.",
"enum": [
"Replacement Not Requested",
"Replacement Requested",
"Replacement Tested",
"Not Reported",
"Other"
],
"type": "string"
},
"sample_volume": {
"description": "Volume of the parent sample (e.g. Heparin tube volume)",
"type": "number"
},
"sample_volume_units": {
"description": "Unit for the parent sample volume.",
"enum": [
"Microliter",
"Milliliter",
"Not Reported",
"Other"
],
"type": "string"
},
"shipping_entry_number": {
"description": "Provides a numbered identifier for patient (sample) entry in a shipment manifest.",
"type": "integer"
},
"site_description": {
"description": "Descritpion of the topography category. e.g LUNG AND BRONCHUS",
"type": "string"
},
"surgical_pathology_report_id": {
"description": "A unique identifier so someone can find the surgical pathology report.",
"encrypt": true,
"type": "string"
},
"topography_code": {
"description": "ICD-0-3 topography site code from which a specimen was isolated. e.g. C34.1",
"type": "string"
},
"topography_description": {
"description": "ICD-0-3 site code description. e.g. Upper lobe, lung",
"type": "string"
},
"tumor_tissue_total_area_percentage": {
"description": "Score the percentage of tumor (including tumor bed) tissue area of the slide (e.g. vs non-malignant or normal tissue)",
"maximum": 100,
"minimum": 0,
"type": "number"
},
"type_of_primary_container": {
"description": "The format in which the sample was sent.",
"enum": [
"Sodium heparin",
"Blood specimen container with EDTA",
"Potassium EDTA",
"Streck Blood Collection Tube",
"Stool collection container with DNA stabilizer",
"Not Reported",
"Other"
],
"type": "string"
},
"type_of_sample": {
"description": "Type of sample sent.",
"enum": [
"Tumor Tissue",
"Normal Tissue",
"Skin Tissue",
"Blood",
"Bone Marrow",
"Cerebrospinal Fluid",
"Lymph Node",
"Stool",
"Not Reported",
"Other"
],
"type": "string"
},
"type_of_tumor_sample": {
"description": "The type of tumor sample obtained (primary or metastatic).",
"enum": [
"Metastatic Tumor",
"Primary Tumor",
"Not Reported",
"Other"
],
"type": "string"
},
"viable_stroma_area_percentage": {
"description": "Score the evaluation of stromal elements (this indicates the % area of tumor bed occupied by non-tumor cells, including inflammatory cells [lymphocytes, histiocytes, etc], endothelial cells, fibroblasts, etc)",
"maximum": 100,
"minimum": 0,
"type": "number"
},
"viable_tumor_area_percentage": {
"description": "Score the percentage of viable tumor cells comprising the tumor bed area",
"maximum": 100,
"minimum": 0,
"type": "number"
}
},
"required": [
"cimac_id",
"parent_sample_id",
"collection_event_name",
"sample_location",
"type_of_sample"
],
"then": {
"required": [
"type_of_primary_container"
]
},
"title": "Sample",
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
}
},
"required": [
"cimac_participant_id",
"participant_id",
"samples"
],
"title": "Participant",
"type": "object"
},
"mergeOptions": {
"idRef": "/cimac_participant_id"
},
"mergeStrategy": "arrayMergeById",
"type": "array"
},
"protocol_identifier": {
"description": "Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412.",
"type": "string"
},
"schema": {
"$id": "image_artifact",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"allOf": [
{
"$id": "artifact_core",
"$schema": "metaschema/strict_meta_schema.json#",
"anyOf": [
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"md5_hash"
]
},
{
"required": [
"object_url",
"uploaded_timestamp",
"file_size_bytes",
"artifact_category",
"crc32c_hash"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Any file artifact associated with a clinical trial.",
"inheritableBase": true,
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"description": "Data Format.",
"enum": [
"FASTA",
"FASTQ.GZ",
"VCF.GZ",
"IMAGE",
"VCF",
"CSV",
"TSV",
"XLSX",
"NPX",
"ELISA",
"BAM",
"BAM.BAI",
"MAF",
"BINARY",
"TEXT",
"ZIP",
"FCS",
"GZ",
"RCC",
"JSON",
"YAML",
"[NOT SET]"
],
"type": "string"
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
}
},
"title": "Artifact Core",
"type": "object"
}
],
"anyOf": [
{
"required": [
"height",
"width",
"channels"
]
},
{
"required": [
"upload_placeholder"
]
}
],
"description": "Information about an image file.",
"mergeStrategy": "objectMerge",
"properties": {
"artifact_category": {
"description": "Artifact category.",
"enum": [
"Assay Artifact from CIMAC",
"Pipeline Artifact",
"Manifest File"
],
"type": "string"
},
"artifact_creator": {
"description": "The name of the center that created this artifact.",
"enum": [
"DFCI",
"Mount Sinai",
"Stanford",
"MD Anderson"
],
"type": "string"
},
"channels": {
"$comment": "3 for RGB imagery, 1 for grayscale imagery.",
"description": "Number of channels in the image.",
"type": "integer"
},
"crc32c_hash": {
"description": "CRC32c Hash of artifact.",
"type": "string"
},
"data_format": {
"const": "IMAGE",
"description": "Data format."
},
"facet_group": {
"description": "The internal data category for this artifact",
"type": "string"
},
"file_name": {
"$comment": "This supposedly get generated from 'gcs_uri_format' field in template schema def.",
"description": "The name of the file with extension.",
"type": "string"
},
"file_size_bytes": {
"description": "File size in bytes.",
"type": "integer"
},
"height": {
"description": "Height of the image.",
"type": "integer"
},
"md5_hash": {
"description": "MD5 Hash of artifact. Not available for composite GCS objects.",
"type": "string"
},
"object_url": {
"description": "URL to artifact within Google Bucket.",
"type": "string"
},
"upload_placeholder": {
"$comment": "It might be something like random uuid or `upload_job_id` to help trace everything back.",
"description": "A placeholder for when artifact file is being uploaded.",
"type": "string"
},
"uploaded_timestamp": {
"description": "Timestamp of when artifact was loaded into the system.",
"format": "date-time",
"type": "string"
},
"uploader": {
"description": "The name of the person uploading the artifact.",
"type": "string"
},
"uuid": {
"description": "UUID of artifact.",
"type": "string"
},
"visible": {
"description": "Indicates if the artifact is visible. If set to false, the artifact is effectively deleted.",
"type": "boolean"
},
"width": {
"description": "Width of the image.",
"type": "integer"
}
},
"title": "Image Artifact",
"type": "object"
},
"shipments": {
"items": {
"$id": "shipping_core",
"$schema": "metaschema/strict_meta_schema.json#",
"additionalProperties": false,
"description": "Core shipping details for a manifest.",
"properties": {
"account_number": {
"description": "Courier account number to pay for shipping if available. Example: 45465732.",
"type": "string"
},
"assay_priority": {
"description": "Priority of the assay as it appears on the intake form.",
"enum": [
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8",
"9",
"10",
"11",
"12",
"13",
"14",
"15",
"Not Reported",
"Other"
],
"type": "string"
},
"assay_type": {
"description": "Assay and sample type used.",
"enum": [
"Olink",
"WES",
"RNAseq",
"IHC",
"CyTOF",
"H&E",
"ELISA",
"mIF",
"mIHC",
"TCRseq"
],
"type": "string"
},
"courier": {
"description": "Courier utilized for shipment.",
"enum": [
"FEDEX",
"USPS",
"UPS",
"Inter-Site Delivery"
],
"type": "string"
},
"date_received": {
"description": "Date of receipt.",
"format": "date",
"type": "string"
},
"date_shipped": {
"description": "Date of shipment.",
"format": "date",
"type": "string"
},
"manifest_id": {
"description": "Filename of the manifest used to ship this sample. Example: E4412_PBMC.",
"type": "string"
},
"quality_of_shipment": {
"description": "Indication that specimens were received in good condition.",
"enum": [
"Specimen shipment received in good condition",
"Specimen shipment received in poor condition",
"Not Reported",
"Other"
],
"type": "string"
},
"receiving_party": {
"description": "Site where sample was shipped to be assayed.",
"enum": [
"MDA_Wistuba",
"MDA_Bernatchez",
"MDA_Al-Atrash",
"MSSM_Gnjatic",
"MSSM_Rahman",
"MSSM_Kim-Schulze",
"MSSM_Bongers",
"DFCI_Wu",
"DFCI_Hodi",
"DFCI_Severgnini",
"DFCI_Livak",
"Broad_Cibulskis",
"Stanf_Maecker",
"Stanf_Bendall",
"NCH",
"Adaptive",
"FNLCR_MoCha"
],
"type": "string"
},
"ship_from": {
"description": "Contact information for shipment.",
"type": "string"
},
"ship_to": {
"description": "Physical shipping address of the destination.",
"type": "string"
},
"shipping_condition": {
"description": "Type of shipment made.",
"enum": [
"Frozen_Dry_Ice",
"Frozen_Shipper",
"Ice_Pack",
"Ambient",
"Not Reported",
"Other"
],
"type": "string"
},
"tracking_number": {
"description": "Air bill number assigned to shipment. Example: 4567788343.",
"type": "string"
}
},
"required": [
"account_number",
"assay_priority",
"assay_type",
"courier",
"date_received",
"date_shipped",
"manifest_id",
"quality_of_shipment",
"ship_from",
"ship_to",
"shipping_condition",
"tracking_number",
"receiving_party"
],
"title": "Core Shipping Details",
"type": "object"
},
"mergeStrategy": "append",
"type": "array"
},
"trial_description": {
"description": "A brief description of the clinical trial.",
"type": "string"
},
"trial_name": {
"description": "Name of clinical trial.",
"type": "string"
},
"trial_organization": {
"description": "Name of the primary organization that oversees the clinical trial. Example: ECOG-ACRIN, SWOG, etc.",
"type": "string"
},
"trial_status": {
"description": "What stage the clinical trial is at in its process.",
"enum": [
"New",
"Ongoing",
"Completed"
],
"type": "string"
}
},
"required": [
"protocol_identifier",
"participants",
"allowed_cohort_names",
"allowed_collection_event_names"
],
"title": "Clinical Trial",
"type": "object"
}